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ProteomicsParadoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains
Protein kinases are crucial regulators of cellular processes, and their dysregulation is frequently associated with human disorders. ATP-competitive type I inhibitors are widely used to block aberrant kinase activity. However, their effect on non-catalytic kinase functions such as conformation and p...
ORGANISM(S): Homo sapiens (Human) 
2026-06-17 | PXD069830 | Pride
Lip-ms Proximity labeling Structural proteomics Ap-ms Bioid 
TranscriptomicsJanus-Like Opposing Roles of CD47 in Autoimmune Brain Inflammation in Human and Mice
Gene transcripts and proteins expressed during disease pathogenesis identify targets for therapy. We performed microarray analysis of histologically characterized multiple sclerosis (MS) brain lesions in comparison with control brain samples to identify differentially expressed molecules. We identif...
ORGANISM(S): Homo sapiens 
2012-06-23 | E-GEOD-38010 | biostudies-arrayexpress
ProteomicsLimited-proteolysis coupled to mass spectrometry (LiP-MS) data on a serially filtered yeast lysate (the FLiP library) and on lysates of wild-type and Gcn5 mutant yeast strains grown under hydroxyurea stress and control conditions. Affinity purification mass spectrometry on Ada3 pulldowns from yeast grown under hydroxyurea stress and control conditions.
We applied serial ultrafiltration and limited proteolysis-coupled mass spectrometry (LiP-MS) to generate an atlas of peptides that act as markers for the formation or dissolution of protein-protein interactions (PPIs). Applied to Saccharomyces cerevisiae, the approach yielded 6,441 candidate PPI mar...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-10-17 | PXD055566 | Pride
Ap-ms Flip-ms Hydroxyurea Ada3 Lip-ms 
ProteomicsA Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases inPlant Nitrogen Signaling part1 AP-MS and TurboID
Nitrogen (N) is of utmost importance for plant growth and development. Multiple studies have shown that N signaling is tightly coupled with carbon (C) levels, but the interplay between C/N metabolism and growth remains largely an enigma. Nonetheless, the protein kinases sucrose non-fermenting 1 (SNF...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2024-11-12 | PXD054489 | Pride
Ap-ms Arabidopsis Tor complex Proximity labeling Snrk1 complex Nitrogen signaling 
ProteomicsAP-MS of helicase Upf1 in PC12 cells
DNA/RNA helicase Upf1 seems to interact with axonal transcripts in response to nerve growth factor (NGF, A. Ludanyi, M. Gaspari and A. Riccio, unpublished data). In order to shed light on Upf1 mechanism of action and to identify potential associations with molecules having cleavage activity, we perf...
ORGANISM(S): Rattus norvegicus (Rat) 
2021-09-10 | PXD023586 | Pride
Protein complex Hud Ago2 Impa1 
ProteomicsHuman, melanoma, p62/SQSTM1, quantitative proteomics
p62/SQSTM1 was identified as a modulator of metastatic genes selectively enriched in melanoma in autophagy independent manner. iTRAQ quantitative proteomic approach was performed in melanoma cell lines (SK-Mel-103 and UACC-62) deficient for p62 to identify downstream effectors of p62. Similar studie...
ORGANISM(S): Homo sapiens (Human) 
2022-02-28 | PXD006650 | Pride
Human Ap-ms P62/sqstm1 Melanoma cell lines Quantitative proteomics Lc-ms/ms 
ProteomicsKIF1A, TANC2, liprin-a2 interactomes identified by AP-MS.
The mechanisms by which motor proteins are loaded on vesicles and how cargos are captured at appropriate sites remain unclear. To better understand how KIF1A-based transport is regulated, we identified the KIF1A interactome and focused on three binding partners, the calcium binding protein Calmoduli...
ORGANISM(S): Rattus norvegicus (Rat) 
2018-07-12 | PXD010080 | Pride
Ap-ms Tanc2 Liprin-a Lc-msms. Kif1a 
ProteomicsHVint validation by AP-MS analysis of HSV-1 VP26
Human herpesviruses are widespread human pathogens with a remarkable impact on worldwide public health. Despite intense decades of research, the molecular details in many aspects of their function remain to be fully characterized. To unravel the details of how these viruses operate a thorough unders...
ORGANISM(S): Homo sapiens (Human) 
2017-02-02 | PXD003599 | Pride
Protein interactions Orbitrap velos Human Herpes simplex virus Virology Interactome 
ProteomicsAP-MS-based interactome analysis of three pairs of N-terminal proteoforms and their canonical protein
N-terminal proteoforms stem from the same gene but differ at their N-terminus, and most of these are found to be truncated, though some are N-terminally extended caused by ribosomes starting translation from codons in the annotated 5’UTR, and/or carry modified N-termini different from those of the c...
ORGANISM(S): Homo sapiens (Human) 
2023-06-08 | PXD039085 | Pride
Protein-protein interaction N-terminal proteoform Ap-ms Flag tagged Lc-ms/ms 
TranscriptomicsTranscription profiling of mouse MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid) or the vehicle control (DMSO) for 18 hours in osteogenic conditions
Background:; Osteoblast differentiation requires the coordinated stepwise expression of multiple genes. Histone deacetylase inhibitors (HDIs) accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs), which alter gene expression by modifying chromati...
ORGANISM(S): Mus musculus 
2008-06-16 | E-GEOD-9247 | biostudies-arrayexpress
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